Starting phenix.real_space_refine on Thu Jul 2 05:46:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w04_65491/07_2026/9w04_65491_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w04_65491/07_2026/9w04_65491.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w04_65491/07_2026/9w04_65491_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w04_65491/07_2026/9w04_65491_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w04_65491/07_2026/9w04_65491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w04_65491/07_2026/9w04_65491.map" } resolution = 2.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 98 5.49 5 Mg 2 5.21 5 S 30 5.16 5 C 3994 2.51 5 N 1287 2.21 5 O 1516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6927 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2412 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 12, 'TRANS': 289} Chain breaks: 1 Chain: "B" Number of atoms: 2468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2468 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 12, 'TRANS': 296} Chain: "C" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 774 Classifications: {'DNA': 1, 'RNA': 36} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 4, 'rna3p_pur': 12, 'rna3p_pyr': 10} Link IDs: {'rna2p': 14, 'rna3p': 22} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 389 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "E" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 242 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "F" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 374 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "G" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 266 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.61, per 1000 atoms: 0.23 Number of scatterers: 6927 At special positions: 0 Unit cell: (86.275, 74.675, 97.875, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 30 16.00 P 98 15.00 Mg 2 11.99 O 1516 8.00 N 1287 7.00 C 3994 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 293.3 milliseconds 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 4 sheets defined 65.1% alpha, 4.6% beta 33 base pairs and 54 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 23 through 27 Processing helix chain 'A' and resid 50 through 59 Processing helix chain 'A' and resid 65 through 97 Processing helix chain 'A' and resid 103 through 134 Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 150 through 161 removed outlier: 3.501A pdb=" N VAL A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 168 through 177 removed outlier: 3.600A pdb=" N LEU A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 185 removed outlier: 3.583A pdb=" N ARG A 185 " --> pdb=" O SER A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 210 Processing helix chain 'A' and resid 217 through 229 Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 253 through 282 removed outlier: 3.685A pdb=" N ARG A 257 " --> pdb=" O LYS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.119A pdb=" N GLY A 306 " --> pdb=" O GLN A 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 23 through 27 Processing helix chain 'B' and resid 50 through 59 Processing helix chain 'B' and resid 65 through 97 Processing helix chain 'B' and resid 103 through 134 Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.504A pdb=" N GLN B 141 " --> pdb=" O ASP B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 161 removed outlier: 3.676A pdb=" N VAL B 154 " --> pdb=" O GLY B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 181 through 185 removed outlier: 3.944A pdb=" N ARG B 185 " --> pdb=" O SER B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 212 removed outlier: 4.032A pdb=" N LYS B 211 " --> pdb=" O ASN B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 230 removed outlier: 3.780A pdb=" N VAL B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 252 No H-bonds generated for 'chain 'B' and resid 250 through 252' Processing helix chain 'B' and resid 253 through 281 removed outlier: 3.646A pdb=" N ARG B 257 " --> pdb=" O LYS B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 293 Processing helix chain 'B' and resid 301 through 305 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 234 through 238 Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AA4, first strand: chain 'B' and resid 234 through 238 291 hydrogen bonds defined for protein. 831 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 158 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 54 stacking parallelities Total time for adding SS restraints: 1.14 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1739 1.33 - 1.45: 1794 1.45 - 1.57: 3486 1.57 - 1.69: 192 1.69 - 1.81: 54 Bond restraints: 7265 Sorted by residual: bond pdb=" C THR A 46 " pdb=" N ARG A 47 " ideal model delta sigma weight residual 1.331 1.266 0.065 1.22e-02 6.72e+03 2.88e+01 bond pdb=" N VAL A 48 " pdb=" CA VAL A 48 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.14e-02 7.69e+03 1.25e+01 bond pdb=" C ARG A 47 " pdb=" N VAL A 48 " ideal model delta sigma weight residual 1.331 1.284 0.047 1.40e-02 5.10e+03 1.12e+01 bond pdb=" C3' DA D 6 " pdb=" O3' DA D 6 " ideal model delta sigma weight residual 1.435 1.477 -0.042 1.30e-02 5.92e+03 1.06e+01 bond pdb=" N VAL B 48 " pdb=" CA VAL B 48 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.20e-02 6.94e+03 9.14e+00 ... (remaining 7260 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 9575 1.59 - 3.17: 519 3.17 - 4.76: 126 4.76 - 6.35: 21 6.35 - 7.93: 10 Bond angle restraints: 10251 Sorted by residual: angle pdb=" CA THR A 46 " pdb=" C THR A 46 " pdb=" N ARG A 47 " ideal model delta sigma weight residual 115.27 121.90 -6.63 1.24e+00 6.50e-01 2.86e+01 angle pdb=" O4' DG D 7 " pdb=" C4' DG D 7 " pdb=" C3' DG D 7 " ideal model delta sigma weight residual 106.00 103.24 2.76 6.00e-01 2.78e+00 2.11e+01 angle pdb=" N3 DT F 7 " pdb=" C4 DT F 7 " pdb=" O4 DT F 7 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" CA ARG A 47 " pdb=" C ARG A 47 " pdb=" N VAL A 48 " ideal model delta sigma weight residual 115.36 121.72 -6.36 1.48e+00 4.57e-01 1.85e+01 angle pdb=" N3 DT F 20 " pdb=" C4 DT F 20 " pdb=" O4 DT F 20 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 ... (remaining 10246 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.11: 3903 35.11 - 70.21: 327 70.21 - 105.32: 16 105.32 - 140.43: 2 140.43 - 175.54: 7 Dihedral angle restraints: 4255 sinusoidal: 2489 harmonic: 1766 Sorted by residual: dihedral pdb=" C4' DT D 12 " pdb=" C3' DT D 12 " pdb=" O3' DT D 12 " pdb=" P DT D 13 " ideal model delta sinusoidal sigma weight residual 220.00 44.46 175.54 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DA D 6 " pdb=" C3' DA D 6 " pdb=" O3' DA D 6 " pdb=" P DG D 7 " ideal model delta sinusoidal sigma weight residual -140.00 29.97 -169.97 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DA F 8 " pdb=" C3' DA F 8 " pdb=" O3' DA F 8 " pdb=" P DA F 9 " ideal model delta sinusoidal sigma weight residual 220.00 50.27 169.73 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 4252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 1079 0.124 - 0.247: 65 0.247 - 0.371: 0 0.371 - 0.494: 0 0.494 - 0.618: 10 Chirality restraints: 1154 Sorted by residual: chirality pdb=" P DT G 29 " pdb=" OP1 DT G 29 " pdb=" OP2 DT G 29 " pdb=" O5' DT G 29 " both_signs ideal model delta sigma weight residual True 2.34 -2.95 -0.62 2.00e-01 2.50e+01 9.54e+00 chirality pdb=" P DT G 34 " pdb=" OP1 DT G 34 " pdb=" OP2 DT G 34 " pdb=" O5' DT G 34 " both_signs ideal model delta sigma weight residual True 2.34 -2.94 -0.61 2.00e-01 2.50e+01 9.29e+00 chirality pdb=" P DC G 32 " pdb=" OP1 DC G 32 " pdb=" OP2 DC G 32 " pdb=" O5' DC G 32 " both_signs ideal model delta sigma weight residual True 2.34 -2.90 -0.56 2.00e-01 2.50e+01 7.86e+00 ... (remaining 1151 not shown) Planarity restraints: 969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C C 8 " -0.046 2.00e-02 2.50e+03 2.40e-02 1.30e+01 pdb=" N1 C C 8 " 0.052 2.00e-02 2.50e+03 pdb=" C2 C C 8 " 0.006 2.00e-02 2.50e+03 pdb=" O2 C C 8 " 0.004 2.00e-02 2.50e+03 pdb=" N3 C C 8 " -0.006 2.00e-02 2.50e+03 pdb=" C4 C C 8 " -0.007 2.00e-02 2.50e+03 pdb=" N4 C C 8 " -0.011 2.00e-02 2.50e+03 pdb=" C5 C C 8 " -0.002 2.00e-02 2.50e+03 pdb=" C6 C C 8 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 52 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.06e+00 pdb=" C ARG A 52 " 0.049 2.00e-02 2.50e+03 pdb=" O ARG A 52 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA A 53 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 46 " 0.013 2.00e-02 2.50e+03 2.53e-02 6.41e+00 pdb=" C THR A 46 " -0.044 2.00e-02 2.50e+03 pdb=" O THR A 46 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG A 47 " 0.016 2.00e-02 2.50e+03 ... (remaining 966 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.27: 7 2.27 - 2.93: 2875 2.93 - 3.59: 10876 3.59 - 4.24: 18716 4.24 - 4.90: 28788 Nonbonded interactions: 61262 Sorted by model distance: nonbonded pdb=" O3' DA F 22 " pdb="MG MG F 101 " model vdw 1.618 2.170 nonbonded pdb=" O3' DT D 22 " pdb="MG MG B 401 " model vdw 1.932 2.170 nonbonded pdb=" NE2 HIS A 58 " pdb="MG MG F 101 " model vdw 1.970 2.250 nonbonded pdb=" OD1 ASP B 30 " pdb="MG MG B 401 " model vdw 2.042 2.170 nonbonded pdb=" OD1 ASP A 30 " pdb="MG MG F 101 " model vdw 2.062 2.170 ... (remaining 61257 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 1 through 290 or resid 298 through 309)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.450 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 7265 Z= 0.484 Angle : 0.877 7.933 10251 Z= 0.624 Chirality : 0.075 0.618 1154 Planarity : 0.005 0.071 969 Dihedral : 22.078 175.535 3115 Min Nonbonded Distance : 1.618 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.58 % Allowed : 13.23 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.33), residues: 605 helix: 2.35 (0.26), residues: 347 sheet: -1.94 (0.91), residues: 20 loop : 0.24 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 97 TYR 0.011 0.001 TYR A 273 PHE 0.007 0.002 PHE B 36 TRP 0.004 0.001 TRP B 309 HIS 0.008 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00647 / 0.48 ( 7265) covalent geometry : angle 0.87737 / 0.62 (10251) hydrogen bonds : bond 0.14480 / 9.47 ( 372) hydrogen bonds : angle 5.23319 / 3.72 ( 989) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.158 Fit side-chains REVERT: A 9 GLN cc_start: 0.8769 (tt0) cc_final: 0.8528 (tm-30) REVERT: A 88 MET cc_start: 0.9426 (tpp) cc_final: 0.9209 (mmm) REVERT: A 170 SER cc_start: 0.9197 (m) cc_final: 0.8885 (m) REVERT: B 60 ILE cc_start: 0.7961 (mm) cc_final: 0.7648 (pt) outliers start: 3 outliers final: 2 residues processed: 64 average time/residue: 0.4414 time to fit residues: 30.0059 Evaluate side-chains 53 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain B residue 290 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 0.0570 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 ASN B 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.093817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.074705 restraints weight = 13702.437| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.81 r_work: 0.3060 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7265 Z= 0.152 Angle : 0.624 9.167 10251 Z= 0.356 Chirality : 0.045 0.332 1154 Planarity : 0.004 0.039 969 Dihedral : 24.275 173.402 1891 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.75 % Allowed : 13.81 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.33), residues: 605 helix: 2.88 (0.26), residues: 346 sheet: -1.18 (0.98), residues: 20 loop : 0.46 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 286 TYR 0.013 0.001 TYR A 95 PHE 0.008 0.001 PHE A 269 TRP 0.006 0.001 TRP B 309 HIS 0.005 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 ( 7265) covalent geometry : angle 0.62396 / 0.36 (10251) hydrogen bonds : bond 0.05264 / 3.52 ( 372) hydrogen bonds : angle 3.78058 / 2.66 ( 989) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.180 Fit side-chains REVERT: A 9 GLN cc_start: 0.8867 (tt0) cc_final: 0.8432 (tm-30) REVERT: A 170 SER cc_start: 0.9121 (m) cc_final: 0.8815 (m) REVERT: A 285 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8807 (t) REVERT: B 32 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7894 (mp) outliers start: 9 outliers final: 5 residues processed: 65 average time/residue: 0.4043 time to fit residues: 28.1689 Evaluate side-chains 54 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 290 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 0.0670 chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 overall best weight: 0.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN A 204 ASN B 12 HIS B 204 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.093917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.074727 restraints weight = 13529.868| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.80 r_work: 0.3059 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7265 Z= 0.149 Angle : 0.594 8.851 10251 Z= 0.337 Chirality : 0.044 0.312 1154 Planarity : 0.004 0.045 969 Dihedral : 24.088 174.310 1889 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.53 % Allowed : 13.23 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.87 (0.33), residues: 605 helix: 3.07 (0.25), residues: 345 sheet: -0.63 (1.06), residues: 20 loop : 0.41 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 286 TYR 0.016 0.001 TYR A 95 PHE 0.009 0.002 PHE A 269 TRP 0.006 0.001 TRP B 309 HIS 0.006 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.15 ( 7265) covalent geometry : angle 0.59383 / 0.34 (10251) hydrogen bonds : bond 0.04816 / 3.22 ( 372) hydrogen bonds : angle 3.57661 / 2.51 ( 989) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.176 Fit side-chains REVERT: A 9 GLN cc_start: 0.8840 (tt0) cc_final: 0.8372 (tm-30) REVERT: A 170 SER cc_start: 0.9141 (m) cc_final: 0.8821 (m) outliers start: 13 outliers final: 5 residues processed: 63 average time/residue: 0.4263 time to fit residues: 28.7832 Evaluate side-chains 52 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 290 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 38 optimal weight: 0.6980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 ASN B 12 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.092882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.073495 restraints weight = 13775.740| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.83 r_work: 0.3032 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7265 Z= 0.181 Angle : 0.606 8.831 10251 Z= 0.342 Chirality : 0.046 0.313 1154 Planarity : 0.004 0.040 969 Dihedral : 23.928 174.245 1889 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.14 % Allowed : 13.23 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.94 (0.33), residues: 605 helix: 3.05 (0.26), residues: 347 sheet: -0.30 (1.14), residues: 20 loop : 0.52 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 286 TYR 0.018 0.002 TYR A 95 PHE 0.009 0.002 PHE A 269 TRP 0.006 0.001 TRP B 309 HIS 0.006 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.18 ( 7265) covalent geometry : angle 0.60648 / 0.34 (10251) hydrogen bonds : bond 0.04857 / 3.24 ( 372) hydrogen bonds : angle 3.52071 / 2.47 ( 989) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.168 Fit side-chains REVERT: A 9 GLN cc_start: 0.8839 (tt0) cc_final: 0.8382 (tm-30) REVERT: A 28 ASP cc_start: 0.8004 (m-30) cc_final: 0.7797 (m-30) REVERT: A 170 SER cc_start: 0.9137 (m) cc_final: 0.8821 (m) REVERT: A 184 ASP cc_start: 0.8316 (t0) cc_final: 0.7906 (t0) outliers start: 11 outliers final: 5 residues processed: 60 average time/residue: 0.4589 time to fit residues: 29.3460 Evaluate side-chains 51 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 290 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 58 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 27 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 ASN B 12 HIS B 204 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.093708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.074400 restraints weight = 13813.394| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.84 r_work: 0.3051 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7265 Z= 0.149 Angle : 0.584 8.885 10251 Z= 0.331 Chirality : 0.044 0.299 1154 Planarity : 0.004 0.039 969 Dihedral : 23.917 175.127 1889 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.95 % Allowed : 14.40 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.04 (0.33), residues: 605 helix: 3.06 (0.25), residues: 350 sheet: -0.22 (1.15), residues: 20 loop : 0.66 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 286 TYR 0.019 0.001 TYR A 95 PHE 0.010 0.002 PHE A 269 TRP 0.005 0.001 TRP B 309 HIS 0.007 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 ( 7265) covalent geometry : angle 0.58376 / 0.33 (10251) hydrogen bonds : bond 0.04494 / 3.01 ( 372) hydrogen bonds : angle 3.44050 / 2.42 ( 989) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.220 Fit side-chains REVERT: A 9 GLN cc_start: 0.8841 (tt0) cc_final: 0.8370 (tm-30) REVERT: A 170 SER cc_start: 0.9123 (m) cc_final: 0.8792 (m) REVERT: A 184 ASP cc_start: 0.8376 (t0) cc_final: 0.8002 (t0) outliers start: 10 outliers final: 5 residues processed: 58 average time/residue: 0.4388 time to fit residues: 27.1598 Evaluate side-chains 51 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 290 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 11 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 HIS A 204 ASN B 12 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.093856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.074444 restraints weight = 13835.737| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.85 r_work: 0.3051 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7265 Z= 0.147 Angle : 0.574 8.876 10251 Z= 0.325 Chirality : 0.043 0.294 1154 Planarity : 0.004 0.038 969 Dihedral : 23.879 175.861 1889 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.14 % Allowed : 14.59 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.14 (0.33), residues: 605 helix: 3.10 (0.25), residues: 349 sheet: -0.04 (1.15), residues: 20 loop : 0.77 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 286 TYR 0.021 0.001 TYR A 95 PHE 0.010 0.002 PHE A 269 TRP 0.005 0.001 TRP B 309 HIS 0.004 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 ( 7265) covalent geometry : angle 0.57353 / 0.33 (10251) hydrogen bonds : bond 0.04411 / 2.96 ( 372) hydrogen bonds : angle 3.36712 / 2.37 ( 989) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.210 Fit side-chains REVERT: A 9 GLN cc_start: 0.8842 (tt0) cc_final: 0.8375 (tm-30) REVERT: A 170 SER cc_start: 0.9128 (m) cc_final: 0.8787 (m) REVERT: A 184 ASP cc_start: 0.8412 (t0) cc_final: 0.8030 (t0) outliers start: 11 outliers final: 7 residues processed: 57 average time/residue: 0.3990 time to fit residues: 24.3000 Evaluate side-chains 53 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 290 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 29 optimal weight: 0.0770 overall best weight: 1.1540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN B 12 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.093979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.074512 restraints weight = 13722.531| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.84 r_work: 0.3051 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7265 Z= 0.149 Angle : 0.567 8.680 10251 Z= 0.322 Chirality : 0.043 0.293 1154 Planarity : 0.004 0.038 969 Dihedral : 23.868 176.636 1889 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.95 % Allowed : 14.59 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.18 (0.33), residues: 605 helix: 3.09 (0.25), residues: 349 sheet: 0.06 (1.14), residues: 20 loop : 0.85 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 286 TYR 0.020 0.001 TYR A 95 PHE 0.011 0.002 PHE A 269 TRP 0.005 0.001 TRP B 309 HIS 0.006 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.15 ( 7265) covalent geometry : angle 0.56674 / 0.32 (10251) hydrogen bonds : bond 0.04378 / 2.94 ( 372) hydrogen bonds : angle 3.36129 / 2.36 ( 989) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.239 Fit side-chains REVERT: A 9 GLN cc_start: 0.8811 (tt0) cc_final: 0.8358 (tm-30) REVERT: A 170 SER cc_start: 0.9124 (m) cc_final: 0.8780 (m) REVERT: A 184 ASP cc_start: 0.8449 (t0) cc_final: 0.8070 (t0) outliers start: 10 outliers final: 8 residues processed: 57 average time/residue: 0.4524 time to fit residues: 27.5862 Evaluate side-chains 58 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 290 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 32 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.0060 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN B 12 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.095634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.076253 restraints weight = 13873.063| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.86 r_work: 0.3089 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7265 Z= 0.125 Angle : 0.543 7.342 10251 Z= 0.311 Chirality : 0.041 0.292 1154 Planarity : 0.004 0.039 969 Dihedral : 23.837 178.829 1889 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.95 % Allowed : 15.56 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.27 (0.33), residues: 605 helix: 3.15 (0.25), residues: 349 sheet: 0.06 (1.13), residues: 20 loop : 0.93 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 286 TYR 0.023 0.001 TYR A 95 PHE 0.010 0.001 PHE A 269 TRP 0.006 0.001 TRP B 309 HIS 0.004 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.12 ( 7265) covalent geometry : angle 0.54279 / 0.31 (10251) hydrogen bonds : bond 0.04089 / 2.75 ( 372) hydrogen bonds : angle 3.25136 / 2.28 ( 989) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.231 Fit side-chains REVERT: A 9 GLN cc_start: 0.8817 (tt0) cc_final: 0.8358 (tm-30) REVERT: A 170 SER cc_start: 0.9116 (m) cc_final: 0.8799 (m) REVERT: A 184 ASP cc_start: 0.8453 (t0) cc_final: 0.8092 (t0) outliers start: 10 outliers final: 8 residues processed: 59 average time/residue: 0.4811 time to fit residues: 30.3646 Evaluate side-chains 57 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 290 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 51 optimal weight: 0.0570 chunk 15 optimal weight: 0.9990 chunk 65 optimal weight: 20.0000 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN A 207 ASN B 12 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.095622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.076296 restraints weight = 13794.389| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.86 r_work: 0.3093 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 7265 Z= 0.128 Angle : 0.560 7.504 10251 Z= 0.318 Chirality : 0.041 0.291 1154 Planarity : 0.004 0.038 969 Dihedral : 23.787 179.459 1889 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.75 % Allowed : 16.73 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.31 (0.33), residues: 605 helix: 3.12 (0.25), residues: 349 sheet: 0.04 (1.14), residues: 20 loop : 1.04 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 286 TYR 0.024 0.001 TYR A 95 PHE 0.008 0.001 PHE A 269 TRP 0.006 0.001 TRP B 274 HIS 0.007 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.13 ( 7265) covalent geometry : angle 0.56015 / 0.32 (10251) hydrogen bonds : bond 0.04080 / 2.74 ( 372) hydrogen bonds : angle 3.25535 / 2.28 ( 989) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.153 Fit side-chains REVERT: A 9 GLN cc_start: 0.8829 (tt0) cc_final: 0.8391 (tm-30) REVERT: A 170 SER cc_start: 0.9129 (m) cc_final: 0.8808 (m) REVERT: A 184 ASP cc_start: 0.8471 (t0) cc_final: 0.8125 (t0) outliers start: 9 outliers final: 7 residues processed: 61 average time/residue: 0.3900 time to fit residues: 25.4304 Evaluate side-chains 55 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 290 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 16 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 chunk 12 optimal weight: 0.1980 chunk 38 optimal weight: 0.8980 chunk 48 optimal weight: 0.0870 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.096488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.077114 restraints weight = 13710.842| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.85 r_work: 0.3111 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7265 Z= 0.120 Angle : 0.539 7.998 10251 Z= 0.307 Chirality : 0.040 0.293 1154 Planarity : 0.004 0.039 969 Dihedral : 23.746 179.266 1889 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.56 % Allowed : 16.93 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.34 (0.33), residues: 605 helix: 3.12 (0.25), residues: 349 sheet: 0.12 (1.19), residues: 20 loop : 1.10 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 286 TYR 0.024 0.001 TYR A 95 PHE 0.008 0.001 PHE A 269 TRP 0.006 0.001 TRP B 274 HIS 0.003 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.12 ( 7265) covalent geometry : angle 0.53857 / 0.31 (10251) hydrogen bonds : bond 0.03946 / 2.66 ( 372) hydrogen bonds : angle 3.21842 / 2.25 ( 989) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.137 Fit side-chains REVERT: A 9 GLN cc_start: 0.8815 (tt0) cc_final: 0.8362 (tm-30) REVERT: A 170 SER cc_start: 0.9124 (m) cc_final: 0.8806 (m) REVERT: A 184 ASP cc_start: 0.8433 (t0) cc_final: 0.8093 (t0) outliers start: 8 outliers final: 7 residues processed: 56 average time/residue: 0.4163 time to fit residues: 24.8480 Evaluate side-chains 55 residues out of total 514 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 290 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 57 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 ASN B 12 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.094407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.074914 restraints weight = 13639.257| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.85 r_work: 0.3065 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7265 Z= 0.158 Angle : 0.565 7.611 10251 Z= 0.320 Chirality : 0.042 0.296 1154 Planarity : 0.004 0.039 969 Dihedral : 23.726 179.569 1889 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.56 % Allowed : 16.34 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.29 (0.33), residues: 605 helix: 3.06 (0.25), residues: 349 sheet: 0.10 (1.15), residues: 20 loop : 1.11 (0.43), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 286 TYR 0.025 0.001 TYR A 95 PHE 0.009 0.001 PHE A 269 TRP 0.005 0.001 TRP B 274 HIS 0.006 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.16 ( 7265) covalent geometry : angle 0.56506 / 0.32 (10251) hydrogen bonds : bond 0.04340 / 2.92 ( 372) hydrogen bonds : angle 3.29588 / 2.30 ( 989) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2344.90 seconds wall clock time: 40 minutes 44.96 seconds (2444.96 seconds total)